Summary Manhattan plots

Interaction test

Interaction test loci
index_var chr pos P_int G-W interaction effect P_joint P_marginal
rs12136785 1 89478687 4.7e-06 FALSE 6.70e-06 0.0884292
rs75242550 2 47777458 9.6e-06 FALSE 3.74e-05 0.4243720
rs12197749 6 146536288 3.1e-06 FALSE 1.92e-05 0.3766780
7:7343876_CA_C 7 7343876 2.4e-06 FALSE 7.80e-06 0.3709310
rs4128327 8 110032847 3.4e-06 FALSE 1.12e-05 0.0793897
rs555728622 10 100281893 5.8e-06 FALSE 2.62e-05 0.8744820
11:6801573_CAAA_C 11 6801573 9.1e-06 FALSE 5.60e-06 0.1917850
rs61944504 13 27321494 2.3e-06 FALSE 1.14e-05 0.3039250
rs4793425 17 70299527 2.9e-06 FALSE 8.40e-06 0.8687370
rs55690660 17 72352686 6.5e-06 FALSE 3.83e-05 0.5641650
rs1053744 22 50885775 6.1e-06 FALSE 1.33e-05 0.1111860
Marginal test loci
index_var chr pos P_marginal
rs116777618 1 205431181 2.5e-06
rs12727804 1 91733994 0.0e+00
rs7367177 1 158045407 8.0e-06
rs758983573 1 14152154 4.8e-06
rs35489748 2 2957848 8.4e-06
rs560385512 2 179548951 4.4e-06
rs115093875 2 188943739 2.1e-06
2:202679672_AT_A 2 202679672 1.9e-06
rs112916110 2 70820996 8.5e-06
rs12465135 2 34017430 1.0e-07
5:125873847_CAAAAAAAAAAAAAA_C 5 125873847 3.9e-06
rs17051780 6 124710492 8.6e-06
rs79981382 6 64606946 5.6e-06
rs71715757 6 164375525 4.7e-06
rs745604245 6 154800208 4.1e-06
rs145332204 7 148066266 2.7e-06
rs703413 10 119311377 9.2e-06
11:1796572_AG_A 11 1796572 3.5e-06
rs11612110 12 9352791 8.4e-06
rs36064217 12 83803246 1.8e-06
12:116391621_TA_T 12 116391621 0.0e+00
rs9545832 13 82247081 2.5e-06
rs61975598 14 92843276 6.7e-06
rs76787529 14 78868119 9.0e-06
rs1243596 14 21072640 5.8e-06
rs66638200 14 33621296 4.7e-06
rs35872736 15 45618301 1.5e-06
rs4300625 15 92257885 2.6e-06
rs73365896 15 29766707 4.6e-06
rs73531463 16 6310835 7.0e-07
rs61190547 16 24032297 4.2e-06
rs76839250 16 90051269 6.0e-07
rs200513128 17 18392377 4.2e-06
rs16973407 19 39913558 3.0e-06

Joint test

Joint test loci
index_var chr pos P_joint Genome-wide joint locus Genome-wide marginal locus
rs12727804 1 91733994 2.87e-08 TRUE TRUE
rs17544265 1 215152131 4.02e-08 TRUE FALSE
rs1491690 3 70131341 9.64e-09 TRUE FALSE
rs4435599 10 42390234 3.42e-08 TRUE FALSE
rs190316617 11 1797388 5.61e-09 TRUE TRUE
rs148035207 16 6330954 6.62e-09 TRUE FALSE
rs73157943 22 25333267 3.01e-09 TRUE FALSE

Summarization report parameters
Parameter Value
chromosome_col CHR
position_col POS
ref_allele_col Non_Effect_Allele
alt_allele_col Effect_Allele
allele_freq_col AF
beta_interaction_col Beta_Interaction_1
p_interaction_col P_Value_Interaction
p_joint_col P_Value_Joint
p_marginal_col P_Value_Marginal
gw_threshold 5e-8
prune_threshold_int 1e-5
prune_threshold_joint 5e-8
prune_locus_width 500000
GEM_file sex_int_res_full
variant_id_col RSID
maf_filter 0.05